GeneTerrain

Category Cross-Omics>Biomarker Discovery/Analysis/Tools and Genomics>Gene Expression Analysis/Profiling

Abstract GeneTerrain(TM) is a next-generation panel biomarker discovery and validation software product.

It is built on the visual metaphor of 3-D visualization of gene/protein expression data, laid out carefully on cartography of molecular interaction network specific to a biological process.

GeneTerrain is a new network visualization technique using scattered data interpolation and surface rendering, based upon a foundation layout of a scalar field.

Contours of the interpolated surfaces are generated to support multi- scale visual interaction for data exploration.

The GeneTerrain framework visualizes quantitative attributes of nodes in a network as a continuous surface by interpolating the scalar field, therefore avoiding scalability issues typical in conventional network visualizations while also maintaining the topological properties of the original network.

GeneTerrain can address biological questions in which correlated functional changes of genes, proteins, and metabolites have to be investigated in the same network context. Examples of these questions are:

1) What are the significant gene expression pattern changes in a given biological condition such as human disease?

2) Where are such changes taking place in the functional context of genes and proteins?

3) Can we see biologically significant changes in gene/protein expression measurements, despite inherent data noise from DNA microarray experiments?

GeneTerrain's novel visualization framework addresses the above biology-inspired knowledge discovery questions/problems using scattered data interpolation, surface rendering, and interactive visual exploration.

This visualization method offers the following advantages:

1) A modified force-direct graph layout model captures the inherent structural properties of original network, which is both edge-weighted and node-weighted.

2) Scattered data interpolation and surface rendering avoid the scalability problem and represent features derived from the data set as prominent geographic landmarks.

3) Interaction with areas and heights supports multi-scale visualization and visual exploration, which can lead to the discovery of new hypotheses based on domain knowledge.

GeneTerrain has been applied to the study of a bio-molecular interaction network integrated with gene expression data for Alzheimer's disease (AD).

In this application, differential gene expression profiles obtained from the human brain are rendered for AD patients with differing degrees of severity and compared to healthy individuals.

This visualization technique is effective in revealing several types of molecular biomarkers, which are traditionally difficult to detect due to noises in data derived from DNA microarray experiments.

GeneTerrain is also being actively used for lung cancer investigation by the bioinformatics group from school of informatics at Indiana University.

The manufacturer is in the process of refining their technique, developing user-friendly software tools, and applying it to other disease biology studies.

The manufacturer believes that the principle and framework of their work can be generalized for biomarker discovery data explorations beyond the case study of Alzheimer’s disease.

In fact, other biological ontology networks, including disease networks, pathway networks, and their dynamics can also be visualized and explored using the GeneTerrain framework, given the appropriate goals of investigation and the definitions of vertices and their relationships in the networks.

By adjusting and enhancing the interactivity of the GeneTerrain framework, the visualization framework can further be incorporated into knowledge discovery processes in biological domains.

GeneTerrain is a research visual analytic platform that is currently still in the research prototyping stage.

The software is free to use by the public. It is copyright protected by the Discovery Informatics and Computing Group at Indiana University.

Note: For additional info on this product see -- GeneTerrain: Visual Exploration of Differential Gene Expression Profiles Organized in Native Biomolecular Interaction Networks (2008) Information Visualization, doi: 10.1057/palgrave.ivs.9500169

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Manufacturer Web Site GeneTerrain

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G6G Abstract Number 20365

G6G Manufacturer Number 104014